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Zelkova schneideriana Hand-Mazz is a second-class key protected wild plant in China. Here, the complete mitochondrial genome of Zelkova schneideriana Hand-Mazz was sequenced using Nanopore Sequel and Illumina NovaSeq platform. The mitochondrial genome was assembled into three circular-mapping molecules with the genome sizes of 154,640 bp, 192,388 bp and 146,907 bp, including 36 protein-coding genes, 19 tRNA genes, and 3 rRNA genes. Phylogenetic analysis indicated that Zelkova schneideriana Hand-Mazz is close with Hemiptelea davidii, a species in same Ulmaceae Mirb.